Islamophobia

This is a goodish article on anti-Muslim discrimination in the US. One aspect I find particularly incomprehensible:

"In America right now, there are intense concerns about many issues -- immigration, the faltering economy, the interminable wars" and the erroneous belief, held by many Americans, that the first nonwhite president is Muslim, said Akbar Ahmed, a professor of Islamic studies at American University.

Do people really feel increased hatred of a group when a (supposed) member is in a position of authority? Why? Wouldn't it make equal sense to believe that, if a Muslim is running the country, they can't be all bad? Or is Obama evidence that a vast Islamic conspiracy is poised to overrun the US, enslaving Christians and probably eating their babies?